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Molecular insights into the dynamics of pharmacogenetically important N-terminal variants of the human β2-adrenergic receptor.

Shahane G, Parsania C, Sengupta D, Joshi M - PLoS Comput. Biol. (2014)

Bottom Line: Our simulations reveal that the N-terminal region of the Arg variant shows greater dynamics than the Gly variant, leading to differential placement.Further, the position and dynamics of the N-terminal region, further, affects the ligand binding-site accessibility.Interestingly, long-range effects are also seen at the ligand binding site, which is marginally larger in the Gly as compared to the Arg variant resulting in the preferential docking of albuterol to the Gly variant.

View Article: PubMed Central - PubMed

Affiliation: CSIR-National Chemical Laboratory, Pune, India.

ABSTRACT
The human β2-adrenergic receptor (β2AR), a member of the G-protein coupled receptor (GPCR) family, is expressed in bronchial smooth muscle cells. Upon activation by agonists, β2AR causes bronchodilation and relief in asthma patients. The N-terminal polymorphism of β2AR at the 16th position, Arg16Gly, has warranted a lot of attention since it is linked to variations in response to albuterol (agonist) treatment. Although the β2AR is one of the well-studied GPCRs, the N-terminus which harbors this mutation, is absent in all available experimental structures. The goal of this work was to study the molecular level differences between the N-terminal variants using structural modeling and atomistic molecular dynamics simulations. Our simulations reveal that the N-terminal region of the Arg variant shows greater dynamics than the Gly variant, leading to differential placement. Further, the position and dynamics of the N-terminal region, further, affects the ligand binding-site accessibility. Interestingly, long-range effects are also seen at the ligand binding site, which is marginally larger in the Gly as compared to the Arg variant resulting in the preferential docking of albuterol to the Gly variant. This study thus reveals key differences between the variants providing a molecular framework towards understanding the variable drug response in asthma patients.

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Related in: MedlinePlus

Structural characterization of the β2AR variants.All atom protein RMSD of (A) Arg and (B) Gly variants of β2AR with respect to the first frame of the production run. All atom RMSD of the N-terminal residues 1 to 29 of (C) Arg and (D) Gly variants of β2AR. RMSF profile of the N-terminal C-alpha atoms of (E) Arg and (F) Gly variants. For each plot, the blue line indicates the first simulation, the red indicates the second and the green line indicates the third simulation.
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pcbi-1004006-g002: Structural characterization of the β2AR variants.All atom protein RMSD of (A) Arg and (B) Gly variants of β2AR with respect to the first frame of the production run. All atom RMSD of the N-terminal residues 1 to 29 of (C) Arg and (D) Gly variants of β2AR. RMSF profile of the N-terminal C-alpha atoms of (E) Arg and (F) Gly variants. For each plot, the blue line indicates the first simulation, the red indicates the second and the green line indicates the third simulation.

Mentions: MD simulations of the variants of β2AR embedded in a lipid bilayer were performed in triplicate to ensure adequate sampling. To characterize the structural variation during the course of the simulation, the RMSD of the entire protein, for each of the six simulations was calculated (Fig. 2 A, B). The RMSD of the Arg variant, overall, is higher than the Gly variant. We further checked the RMSD of the TM helices, ICL3 and the N-terminal residues, separately to assess the contributions of the different regions of the receptor to the observed variation in RMSD for the entire protein. The TM helices were found to be stable over the simulation time (S2 Figure). Interestingly, the RMSD of the ICL3 is slightly higher in the simulations of the Arg variant as compared to the Gly variant (S2 Figure). The RMSD profiles of the N-terminal region (residue 1 to 28) reveal significant differences across the variants (Fig. 2 C, D). The three simulations of the Arg variant exhibit, on an average, a higher RMSD than the Gly variants suggesting enhanced dynamics. The large increase in the RMSD of the N-terminal region of the Arg variants contributes to the higher RMSD of the whole protein seen earlier. To understand the residue wise contribution of the N-terminal region to the conformational sampling we calculated the per-residue fluctuations over the simulations (Fig. 2 E, F). Consistent with the RMSD plots, the fluctuations of the residues in the Arg variants are generally higher. The first ten residues of the Arg variants show higher fluctuations than the corresponding residues in the Gly variant, specifically large differences are observed between residues 5–10.


Molecular insights into the dynamics of pharmacogenetically important N-terminal variants of the human β2-adrenergic receptor.

Shahane G, Parsania C, Sengupta D, Joshi M - PLoS Comput. Biol. (2014)

Structural characterization of the β2AR variants.All atom protein RMSD of (A) Arg and (B) Gly variants of β2AR with respect to the first frame of the production run. All atom RMSD of the N-terminal residues 1 to 29 of (C) Arg and (D) Gly variants of β2AR. RMSF profile of the N-terminal C-alpha atoms of (E) Arg and (F) Gly variants. For each plot, the blue line indicates the first simulation, the red indicates the second and the green line indicates the third simulation.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263363&req=5

pcbi-1004006-g002: Structural characterization of the β2AR variants.All atom protein RMSD of (A) Arg and (B) Gly variants of β2AR with respect to the first frame of the production run. All atom RMSD of the N-terminal residues 1 to 29 of (C) Arg and (D) Gly variants of β2AR. RMSF profile of the N-terminal C-alpha atoms of (E) Arg and (F) Gly variants. For each plot, the blue line indicates the first simulation, the red indicates the second and the green line indicates the third simulation.
Mentions: MD simulations of the variants of β2AR embedded in a lipid bilayer were performed in triplicate to ensure adequate sampling. To characterize the structural variation during the course of the simulation, the RMSD of the entire protein, for each of the six simulations was calculated (Fig. 2 A, B). The RMSD of the Arg variant, overall, is higher than the Gly variant. We further checked the RMSD of the TM helices, ICL3 and the N-terminal residues, separately to assess the contributions of the different regions of the receptor to the observed variation in RMSD for the entire protein. The TM helices were found to be stable over the simulation time (S2 Figure). Interestingly, the RMSD of the ICL3 is slightly higher in the simulations of the Arg variant as compared to the Gly variant (S2 Figure). The RMSD profiles of the N-terminal region (residue 1 to 28) reveal significant differences across the variants (Fig. 2 C, D). The three simulations of the Arg variant exhibit, on an average, a higher RMSD than the Gly variants suggesting enhanced dynamics. The large increase in the RMSD of the N-terminal region of the Arg variants contributes to the higher RMSD of the whole protein seen earlier. To understand the residue wise contribution of the N-terminal region to the conformational sampling we calculated the per-residue fluctuations over the simulations (Fig. 2 E, F). Consistent with the RMSD plots, the fluctuations of the residues in the Arg variants are generally higher. The first ten residues of the Arg variants show higher fluctuations than the corresponding residues in the Gly variant, specifically large differences are observed between residues 5–10.

Bottom Line: Our simulations reveal that the N-terminal region of the Arg variant shows greater dynamics than the Gly variant, leading to differential placement.Further, the position and dynamics of the N-terminal region, further, affects the ligand binding-site accessibility.Interestingly, long-range effects are also seen at the ligand binding site, which is marginally larger in the Gly as compared to the Arg variant resulting in the preferential docking of albuterol to the Gly variant.

View Article: PubMed Central - PubMed

Affiliation: CSIR-National Chemical Laboratory, Pune, India.

ABSTRACT
The human β2-adrenergic receptor (β2AR), a member of the G-protein coupled receptor (GPCR) family, is expressed in bronchial smooth muscle cells. Upon activation by agonists, β2AR causes bronchodilation and relief in asthma patients. The N-terminal polymorphism of β2AR at the 16th position, Arg16Gly, has warranted a lot of attention since it is linked to variations in response to albuterol (agonist) treatment. Although the β2AR is one of the well-studied GPCRs, the N-terminus which harbors this mutation, is absent in all available experimental structures. The goal of this work was to study the molecular level differences between the N-terminal variants using structural modeling and atomistic molecular dynamics simulations. Our simulations reveal that the N-terminal region of the Arg variant shows greater dynamics than the Gly variant, leading to differential placement. Further, the position and dynamics of the N-terminal region, further, affects the ligand binding-site accessibility. Interestingly, long-range effects are also seen at the ligand binding site, which is marginally larger in the Gly as compared to the Arg variant resulting in the preferential docking of albuterol to the Gly variant. This study thus reveals key differences between the variants providing a molecular framework towards understanding the variable drug response in asthma patients.

Show MeSH
Related in: MedlinePlus